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- PDB-4o1o: Crystal Structure of RNase L in complex with 2-5A -

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Basic information

Entry
Database: PDB / ID: 4o1o
TitleCrystal Structure of RNase L in complex with 2-5A
ComponentsRibonuclease L
KeywordsTRANSFERASE / HYDROLASE / ankyrin repeat-kinase-RNAse / 2-5A
Function / homology
Function and homology information


RNA nuclease activity / mRNA processing / protein kinase activity / ATP binding / metal ion binding
Similarity search - Function
RNase L, RNase domain / KEN domain / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ankyrin repeats (many copies) / Ankyrin repeat / de novo design (two linked rop proteins) ...RNase L, RNase domain / KEN domain / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ankyrin repeats (many copies) / Ankyrin repeat / de novo design (two linked rop proteins) / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-25L / Ribonuclease L
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsHuang, H. / Zeqiraj, E. / Ceccarelli, D.F. / Sicheri, F.
CitationJournal: Mol.Cell / Year: 2014
Title: Dimeric structure of pseudokinase RNase L bound to 2-5A reveals a basis for interferon-induced antiviral activity.
Authors: Huang, H. / Zeqiraj, E. / Dong, B. / Jha, B.K. / Duffy, N.M. / Orlicky, S. / Thevakumaran, N. / Talukdar, M. / Pillon, M.C. / Ceccarelli, D.F. / Wan, L.C. / Juang, Y.C. / Mao, D.Y. / ...Authors: Huang, H. / Zeqiraj, E. / Dong, B. / Jha, B.K. / Duffy, N.M. / Orlicky, S. / Thevakumaran, N. / Talukdar, M. / Pillon, M.C. / Ceccarelli, D.F. / Wan, L.C. / Juang, Y.C. / Mao, D.Y. / Gaughan, C. / Brinton, M.A. / Perelygin, A.A. / Kourinov, I. / Guarne, A. / Silverman, R.H. / Sicheri, F.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease L
B: Ribonuclease L
C: Ribonuclease L
D: Ribonuclease L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,9748
Polymers325,3114
Non-polymers4,6624
Water00
1
A: Ribonuclease L
B: Ribonuclease L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,9874
Polymers162,6562
Non-polymers2,3312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ribonuclease L
D: Ribonuclease L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,9874
Polymers162,6562
Non-polymers2,3312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.792, 111.968, 268.465
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 22 - 729 / Label seq-ID: 7 - 714

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Ribonuclease L


Mass: 81327.836 Da / Num. of mol.: 4 / Fragment: UNP residues 21-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: RNASEL / Production host: Escherichia coli (E. coli) / References: UniProt: A5H025
#2: Chemical
ChemComp-25L / [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate / 2'-5'-oligoadenylate trimer


Mass: 1165.593 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H40N15O25P5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5 mM DTT, 18% PEG2000, 100 mM NaCl, and 100 mM SPG buffer, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.476
11-h,-k,l20.524
ReflectionResolution: 3.25→49.7 Å / Num. all: 54420 / Num. obs: 51209 / % possible obs: 94.1 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6
Reflection shellResolution: 3.267→3.352 Å / % possible all: 92.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4O1P

4o1p


Resolution: 3.27→49.7 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.867 / SU B: 17.906 / SU ML: 0.328 / Cross valid method: THROUGHOUT / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28851 1587 3.1 %RANDOM
Rwork0.23048 ---
all0.23225 52702 --
obs0.23225 49593 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 128.149 Å2
Baniso -1Baniso -2Baniso -3
1-72.54 Å20 Å2-16.7 Å2
2---18.64 Å20 Å2
3----53.9 Å2
Refinement stepCycle: LAST / Resolution: 3.27→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21397 0 300 0 21697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01922104
X-RAY DIFFRACTIONr_bond_other_d0.0050.0220958
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.97529903
X-RAY DIFFRACTIONr_angle_other_deg0.948348165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63352666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64824.7121112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.565153943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.86515152
X-RAY DIFFRACTIONr_chiral_restr0.0690.23298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224966
X-RAY DIFFRACTIONr_gen_planes_other0.0040.025098
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it11.72112.71510727
X-RAY DIFFRACTIONr_mcbond_other11.72112.71410726
X-RAY DIFFRACTIONr_mcangle_it18.31519.01613372
X-RAY DIFFRACTIONr_mcangle_other18.31419.01613373
X-RAY DIFFRACTIONr_scbond_it10.36913.07411377
X-RAY DIFFRACTIONr_scbond_other10.35413.07211371
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.47719.44416522
X-RAY DIFFRACTIONr_long_range_B_refined29.04892808
X-RAY DIFFRACTIONr_long_range_B_other29.0492801
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A435330.04
12B435330.04
21A433700.04
22C433700.04
31A432360.05
32D432360.05
41B433700.04
42C433700.04
51B432660.05
52D432660.05
61C430930.05
62D430930.05
LS refinement shellResolution: 3.27→3.352 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 119 -
Rwork0.29 2997 -
obs--76.9 %

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